Your store must be configured to auto-apply tax profiles. Otherwise, tax profiles are manually added to the invoice after it has been converted from a customer order. See the article How to apply a tax profile to an invoice.
I sell across multiple jurisdictions and use GlobalTill Tax Profiles. What can I do if the tax profiles fail to auto-apply to the Shopify customer orders upon conversion to an invoice?
The tax rate name in Shopify must match the tax rate name in GlobalTill. If a tax rate was recently renamed in Shopify, update the name in GlobalTill to match and the functionality should resume.